Maybe I'm missing something, but it looks to me like you have a problem with your first snippet:

    while (<open>)
    {   
        ($name, $ID) = (split)...;
         $data{$file} = {$ID => $name};
    }
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In each iteration of that loop, the value of the hash element "$data{$file}" is being replaced by a new anonymous hash, containing a just single "$ID, $name" tuple -- and the previous "$ID, name" are discarded. Don't you want the HoH to have a more than one key in the second-layer hash? I would have expected something like this:

    while (<open>)
    {   
        ($name, $ID) = (split)...;
         $data{$file}{$ID} = $name;
    }
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